def top_level(self, request, api_name=None):
"""
A view that returns a serialized list of all DAS_sources in registers.
"""
sources = self._registry
if request.GET:
form = DASSourcesForm(request.GET)
if form.is_valid():
version = form.cleaned_data['version']
capability = form.cleaned_data['capability']
authority = form.cleaned_data['authority']
stype = form.cleaned_data['type']
organism = form.cleaned_data['organism']
else:
# :TODO raise exception
pass
sources = dict((key, value) for key, value in sources.items() if \
value._meta.version == int(version))
else:
pass
if api_name is None:
api_name = self.api_name
#desired_format = determine_format(request, serializer)
desired_format = 'application/xml'
options = {}
response = HttpResponse(
content=top_level_serializer(sources),
content_type=build_content_type(desired_format))
response = add_das_headers(response, self.version)
return response
def top_level(self, request, api_name=None):
"""
A view that returns a serialized list of all DAS_sources in registers.
"""
sources = self._registry
if request.GET:
form = DASSourcesForm(request.GET)
if form.is_valid():
version = form.cleaned_data['version']
capability = form.cleaned_data['capability']
authority = form.cleaned_data['authority']
stype = form.cleaned_data['type']
organism = form.cleaned_data['organism']
else:
# :TODO raise exception
pass
sources = dict((key, value) for key, value in sources.items() if \
value._meta.version == int(version))
else: pass
if api_name is None:
api_name = self.api_name
#desired_format = determine_format(request, serializer)
desired_format = 'application/xml'
options = {}
response = HttpResponse(content = top_level_serializer(sources),
content_type=build_content_type(desired_format))
response = add_das_headers(response, self.version)
return response
def get_features(self, request, **kwargs):
""" Returns a DAS GFF xml.
Calls ''obj_get'' to fetch only the objects requested. This method
only responds to HTTP GET.
Similar to obj_get_list in ModelResource with modifications. Need to
make this a factory so that specific fields and be mapped to the
segment and start end.
"""
if hasattr(request, 'GET'):
reference, start, stop = parse_das_segment(request)
query_seg = {'id': reference, 'start':start, 'stop':stop}
query_method = getattr(self, "%s_query" % self._meta.filetype, None)
if query_method:
hits = query_method(**query_seg)
else:
raise NotImplementedError("No query function implemented for\
filetype %s" % self._meta.filetyp)
#:TODO implement json return as well.
try:
content = feature_serializer(request, hits, format_json = getattr(self._meta , 'json'), **query_seg)
except:
content = feature_serializer(request, hits, **query_seg)
response = HttpResponse(content = content,
content_type = 'application/xml')
response = add_das_headers(response)
return response
def get_types(self, request, **kwargs):
registry = {getattr(self._meta , 'resource_name'): self}
content = serializers.type_serializer(request)
response = HttpResponse(
content = content,
content_type = 'application/xml')
response = add_das_headers(response)
return response
def get_features(self, request, **kwargs):
""" Returns a DAS GFF xml.
Calls ''obj_get'' to fetch only the objects requested. This method
only responds to HTTP GET.
Similar to obj_get_list in ModelResource with modifications. Need to
make this a factory so that specific fields and be mapped to the
segment and start end.
"""
if hasattr(request, 'GET'):
reference, start, stop = parse_das_segment(request)
query_seg = {'id': reference, 'start':start, 'stop':stop}
# Attempts to be smart about field mapping
# :TODO implement this
if 'chrom' in self.fields:
pass
# :TODO Need to implement type, category, feature_id and maxbins
# :TODO Check if model has a Kent bin. Also benchmark using this overa
# standard index.
# :TODO make reference more general
try:
reference = int(reference)
except ValueError:
# For when the query is 'chr1'
reference = reference
self.is_authenticated(request)
# Check if there is a binning scheme. Assume it follows the
# UCSC binning scheme.
try:
if start:
base_object_list = self.get_object_list(request).filter(
Q(start__range=(start,stop)) |\
Q(end__range=(start,stop)),
chrom__exact = reference)
else:
base_object_list = self.get_object_list(request).filter(
chrom__exact = reference)
# :TODO authorization check
except ValueError:
raise ValueError('Invalid Request')
# Do I need to convert to a bundle, or too much.
'''
bundles = [self.build_bundle(obj=obj, request=request) for obj in\
base_object_list]
to_be_serialized = [self.full_dehydrate(bundle) for bundle in bundles]
'''
try:
content = feature_serializer(request, base_object_list, format_json = getattr(self._meta , 'json'), **query_seg)
except:
content = feature_serializer(request, base_object_list, **query_seg)
response = HttpResponse(content = content,
content_type = 'application/xml')
response = add_das_headers(response)
return response
def get_list(self, request, **kwargs):
""" Replaces the standard resource response with the sources one.
"""
# :TODO modify top_level_serializer or pass a list with self as
# argument?
registry = {getattr(self._meta, "resource_name"): self}
content = serializers.top_level_serializer(registry)
response = HttpResponse(content=content, content_type="application/xml")
response = add_das_headers(response)
return response
def get_list(self, request, **kwargs):
""" Replaces the standard resource response with the sources one.
"""
# :TODO modify top_level_serializer or pass a list with self as
# argument?
registry = {getattr(self._meta , 'resource_name'): self}
content = serializers.top_level_serializer(registry)
response = HttpResponse(
content = content,
content_type = 'application/xml')
response = add_das_headers(response)
return response
def get_features(self, request, **kwargs):
""" Returns a DAS GFF xml.
Calls ''obj_get'' to fetch only the objects requested. This method
only responds to HTTP GET.
Similar to obj_get_list in ModelResource with modifications. Need to
make this a factory so that specific fields and be mapped to the
segment and start end.
"""
if hasattr(request, 'GET'):
reference, start, stop = parse_das_segment(request)
query_seg = {'id': reference, 'start':start, 'stop':stop}
if 'chrom' in self.fields:
pass
try:
reference = int(reference)
except ValueError:
reference = reference
self.is_authenticated(request)
# :TODO put this throught the regular filter
try:
if start:
base_object_list = self.get_object_list(request).filter(
Q(start__range=(start, stop)) |\
Q(end__range=(start, stop)),
chrom__exact = reference)
else:
base_object_list = self.get_object_list(request).filter(
chrom__exact = reference)
# :TODO authorization check
except ValueError:
raise ValueError('Invalid Request')
bundles = [self.build_bundle(obj=obj, request=request) for obj in\
base_object_list]
to_be_serialized = [self.full_dehydrate(bundle) for bundle in bundles]
# passing reqeust into options is, maybe I should pass in the whole
# request?
options = {'query': query_seg,
'method': self._meta.method,
'request_string': request.META['QUERY_STRING'],
'request_path': request.path,
}
content = self.serialize(request, to_be_serialized, 'xml',
options=options)
response = HttpResponse(content = content,
content_type = 'application/xml')
response = add_das_headers(response)
return response
def get_features(self, request, **kwargs):
""" Returns a DAS GFF xml.
Calls ''obj_get'' to fetch only the objects requested. This method
only responds to HTTP GET.
Similar to obj_get_list in ModelResource with modifications. Need to
make this a factory so that specific fields can be mapped to the
segment and start end.
"""
if hasattr(request, "GET"):
reference, start, stop = parse_das_segment(request)
query_seg = {"id": self._meta.ref_prefix + reference, "start": start, "stop": stop}
query_method = getattr(self, "%s_query" % self._meta.filetype, None)
if query_method:
hits = query_method(**query_seg)
else:
raise NotImplementedError(
"No query function implemented for\
filetype %s"
% self._meta.filetype
)
options = {
"query": query_seg,
"method": self._meta.method,
"request_string": request.META["QUERY_STRING"],
"request_path": request.path,
}
"""
to_be_serialized = [self.build_bundle(data = i.__dict__,
request=request) for i in hits]
content = feature_serializer(request, hits, **query_seg)
"""
to_be_serialized = []
for i in hits:
to_be_serialized.append(Bundle(data=i.__dict__, request=request))
# self.full_dehydrate(hits)
content = self.serialize(request, to_be_serialized, "xml", options=options)
response = HttpResponse(content=content, content_type="application/xml")
response = add_das_headers(response)
return response
def get_stylesheet(self, request, **kwargs):
registry = {getattr(self._meta, "resource_name"): self}
content = serializers.bam_stylesheet(request)
response = HttpResponse(content=content, content_type="application/xml")
response = add_das_headers(response)
return response